SARS_COV_2_ORF1AB_MUSCLE_MView
Reference sequence (1): ORF1AB_China_Dec2019a
Identities normalised by aligned length.
Colored by: identity
                                                cov    pid    1 [        .         .         .         .         :         .         .         .         .         1         .         . 120 
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSEARTAPHGHVMVELVA-----ELEGI     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPH-----ELVA-----ELEGI     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRS-ARTAPHGHVMVELVA-----ELEGI     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      -MSFVAGVTAQGARGTYRAALNSEKHQDHVSLTVPLC--------GSGNLVEKL----SPWFMDGENAY-EVVKAMLLKKEPLLYVPIRLAGHTRHLPGPRVYLVERLIACENPFMVNQL     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      -MSFVAGVTAQGARGTYRAALNSEKHQDHVSLTVPLC--------GSGNLVEKL----SPWFMDGENAY-EVVKAMLLKKEPLLYVPIRLAGHTRHLPGPRVYLVERLIACENPFMVNQL     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      -MSFVAGVTAQGARGTYRAALNSEKHQDHVSLTVPLC--------GSGNLVEKL----SPWFMDGENAY-EVVKAMLLKKEPLLYVPIRLAGHTRHLPGPRVYLVERLIACENPFMVNQL     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      -MSFVAGVTAQGARGTYRAALNSEKHQDHVSLTVPLC--------GSGNLVEKL----SPWFMDGENAY-EVVKAMLLKKEPLLYVPIRLAGHTRHLPGPRVYLVERLIACENPFMVNQL     
   consensus/100%                                               ..ShVsGhstps................HVpLolPlh........G.Gs.VEcl....p.ahhDGpsuh.EV.KuhL....P.L..Phhhht+o.thsuP+.....cLlA......lptl     
   consensus/90%                                                MESLVPGFNEKT................HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL....PQLEQPYVFIKRScARTAPHsalh.ELVA.....ELEGI     
   consensus/80%                                                MESLVPGFNEKT................HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL....PQLEQPYVFIKRSDARTAPHGHVMVELVA.....ELEGI     
   consensus/70%                                                MESLVPGFNEKT................HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL....PQLEQPYVFIKRSDARTAPHGHVMVELVA.....ELEGI     

                                                cov    pid  121          .         .         :         .         .         .         .         2         .         .         .         . 240 
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYG---ADLDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      AYSSSANGSLVGTTLQGKPIGMFFPYDIELVTGKQNILLRKYGR---GGYHY----TPFHYERDNTSCP--EWMDDFEADPKGKYAQNLLKKLIGGDVTP-VDQYMCGVDGKPISAYAFL     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      AYSSSANGSLVGTTLQGKPIGMFFPYDIELVTGKQNILLRKYGR---GGYHY----TPFHYERDNTSCP--EWMDDFEADPKGKYAQNLLKKLIGGDVTP-VDQYMCGVDGKPISAYAFL     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      AYSSSANGSLVGTTLQGKPIGMFFPYDIELVTGKQNILLRKYGR---GGYHY----TPFHYERDNTSCP--EWMDDFEADPKGKYAQNLLKKLIGGDVTP-VDQYMCGVDGKPISAYAFL     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      AYSSSANGSLVGTTLQGKPIGMFFPYDIELVTGKQNILLRKYGR---GGYHY----TPFHYERDNTSCP--EWMDDFEADPKGKYAQNLLKKLIGGDVTP-VDQYMCGVDGKPISAYAFL     
   consensus/100%                                               tYupS...........GcslGhhhPashElssuhpplLLRK.Gp...GGapY....tshchtc-.sosP..-a.-sapsc.puthsppLh+cL.GGshT..VDp.hCGsDGhPlpsht.L     
   consensus/90%                                                QYGRS...........GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYG...psFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
   consensus/80%                                                QYGRS...........GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     
   consensus/70%                                                QYGRS...........GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL     

                                                cov    pid  241          :         .         .         .         .         3         .         .         .         .         :         . 360 
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      MAKDGITKLADVEADVAARADDEGFITLKNNLYRLVWHVERKDVPYPKQSIFTINSVVQKDGVENTPPHY-FTLGCKILTLTPRNKWSGVSDLSLKQKLLYTFYGKESLENPTYIYHSAF     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      MAKDGITKLADVEADVAARADDEGFITLKNNLYRLVWHVERKDVPYPKQSIFTINSVVQKDGVENTPPHY-FTLGCKILTLTPRNKWSGVSDLSLKQKLLYTFYGKESLENPTYIYHSAF     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      MAKDGITKLADVEADVAARADDEGFITLKNNLYRLVWHVERKDVPYPKQSIFTINSVVQKDGVENTPPHY-FTLGCKILTLTPRNKWSGVSDLSLKQKLLYTFYGKESLENPTYIYHSAF     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      MAKDGITKLADVEADVAARADDEGFITLKNNLYRLVWHVERKDVPYPKQSIFTINSVVQKDGVENTPPHY-FTLGCKILTLTPRNKWSGVSDLSLKQKLLYTFYGKESLENPTYIYHSAF     
   consensus/100%                                               hA+sGhsp.sslptplshhssccGhhsh+pp.aclsWasERp-hsY.hQo.FpIp.shphDshpspsPpa.FsLsshIhTlpPRschptlssh.h+.+.lYshhu.pp...ss.hhhSsh     
   consensus/90%                                                LARAGKAS.CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE...CNQMCLSTL     
   consensus/80%                                                LARAGKAS.CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE...CNQMCLSTL     
   consensus/70%                                                LARAGKAS.CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE...CNQMCLSTL     

                                                cov    pid  361          .         .         .         4         .         .         .         .         :         .         .         . 480 
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRANANIGCN     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      IECGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSERC-NVIADSKSFTLIFGGVAYAYFGCEEGTMYFVPRAKSVVSRI     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      IECGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSERC-NVIADSKSFTLIFGGVAYAYFGCEEGTMYFVPRAKSVVSRI     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      IECGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSERC-NVIADSKSFTLIFGGVAYAYFGCEEGTMYFVPRAKSVVSRI     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      IECGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSERC-NVIADSKSFTLIFGGVAYAYFGCEEGTMYFVPRAKSVVSRI     
   consensus/100%                                               hcCspCGpsSW.TGshlpuhsphCGsp.hsp-.tsposGhl..NAllphhCP.....uCpssphts.tpLspYhsEps.psIhcptuhTlhFGGssauYhGCcptshYaVPRApuslup.     
   consensus/90%                                                MKCDHCGETSWQTGDFVKATCEFCGTENLTKE.GATTCGYLPQNAVVKIYCP.....ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRAsANIGCN     
   consensus/80%                                                MKCDHCGETSWQTGDFVKATCEFCGTENLTKE.GATTCGYLPQNAVVKIYCP.....ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     
   consensus/70%                                                MKCDHCGETSWQTGDFVKATCEFCGTENLTKE.GATTCGYLPQNAVVKIYCP.....ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN     

                                                cov    pid  481          .         5         .         .         .         .         :         .         .         .         .         6 600 
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      GDSIF-TGCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYAAITAPYVVLTGLGESFKKV     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      GDSIF-TGCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYAAITAPYVVLTGLGESFKKV     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      GDSIF-TGCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYAAITAPYVVLTGLGESFKKV     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      GDSIF-TGCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYAAITAPYVVLTGLGESFKKV     
   consensus/100%                                               tsulh.pGspG..splhpI....LpppphslNhVG-FhlN-.lhhILuuhossssthhphlKGlshcth+phltsh.shtVTtG.hhcsAhNlG....p.tuIhuPhhshs..uEuh+hV     
   consensus/90%                                                HTGVVGEGSEGLNDNLLEI....LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG....EQKSILSPLYAFA..SEAARVV     
   consensus/80%                                                HTGVVGEGSEGLNDNLLEI....LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG....EQKSILSPLYAFA..SEAARVV     
   consensus/70%                                                HTGVVGEGSEGLNDNLLEI....LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG....EQKSILSPLYAFA..SEAARVV     

                                                cov    pid  601          .         .         .         .         :         .         .         .         .         7         .         . 720 
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ATIPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSELLFDCV----DLSVASTYFLVRL---LQDKTGDFMSTIITSCQTAVSKLLDTCFEATEATFNFLLDLAGLFRIFLRNAYV     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      ATIPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSELLFDCV----DLSVASTYFLVRL---LQDKTGDFMSTIITSCQTAVSKLLDTCFEATEATFNFLLDLAGLFRIFLRNAYV     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ATIPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSELLFDCV----DLSVASTYFLVRL---LQDKTGDFMSTIITSCQTAVSKLLDTCFEATEATFNFLLDLAGLFRIFLRNAYV     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      ATIPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSELLFDCV----DLSVASTYFLVRL---LQDKTGDFMSTIITSCQTAVSKLLDTCFEATEATFNFLLDLAGLFRIFLRNAYV     
   consensus/100%                                               toI..+shpospsolphht+usl......sh.sGlSpaS.hLhDsh....DLussshhhhshl...l.phTupahosIhsos.ptlp.lLDhh.EthctshpFLhDhhtlh+hh.psAh.     
   consensus/90%                                                RSIFSRTLETAQNSVRVLQKAAI......TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
   consensus/80%                                                RSIFSRTLETAQNSVRVLQKAAI......TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     
   consensus/70%                                                RSIFSRTLETAQNSVRVLQKAAI......TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE     

                                                cov    pid  721          .         .         :         .         .         .         .         8         .         .         .         . 840 
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      YTSQGFVVVNGKVSTLVKQVLDLLNKGMQLLHTKVSWAGSNISAVIYSGRESLIFPSGTYY-CVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVSVTVSSNMVETVVGQLEQTN     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      YTSQGFVVVNGKVSTLVKQVLDLLNKGMQLLHTKVSWAGSNISAVIYSGRESLIFPSGTYY-CVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVSVTVSSNMVETVVGQLEQTN     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      YTSQGFVVVNGKVSTLVKQVLDLLNKGMQLLHTKVSWAGFNISAVIYSGRESLIFPSGTYY-CVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVSVTVSSNMVETVVGQLEQTN     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      YTSQGFVVVNGKVSTLVKQVLDLLNKGMQLLHTKVSWAGFNISAVIYSGRESLIFPSGTYY-CVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVSVTVSSNMVETVVGQLEQTN     
   consensus/100%                                               hsutthVssstclpp.VpphhcLlNKhhtLhtspl.huG.plpA.l..Gcp.lhaspGhYh.CVpo+.....p-hsllhPhchsKc.lhL.....pupTlsspV.op.V.hhsGpLp.hp     
   consensus/90%                                                IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA.LNLGETFVTHSKGLYRKCVKSR.....EETGLLMPLKAPKEIIFL.....EGETLPTEVLTEEVVLKTGDLQPLE     
   consensus/80%                                                IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA.LNLGETFVTHSKGLYRKCVKSR.....EETGLLMPLKAPKEIIFL.....EGETLPTEVLTEEVVLKTGDLQPLE     
   consensus/70%                                                IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA.LNLGETFVTHSKGLYRKCVKSR.....EETGLLMPLKAPKEIIFL.....EGETLPTEVLTEEVVLKTGDLQPLE     

                                                cov    pid  841          :         .         .         .         .         9         .         .         .         .         :         . 960 
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGSAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      MHSPDVI----VGDYVIISEKLFVRSKEEDGFAFYPACTNGHAVPTLFRLKGGAPVKKVAFGGDQVHEVAAVRSVTVEYNIHAVLDTLLASSSLRTFVVDKSLSIEEFADVVKEQVSDLL     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      MHSPDVI----VGDYVIISEKLFVRSKEEDGFAFYPACTNGHAVPTLFRLKGGAPVKKVAFGGDQVHEVAAVRSVTVEYNIHAVLDTLLASSSLRTFVVDKSLSIEEFADVVKEQVSDLL     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      MHSPDVI----VGDYVIISEKLFVRSKEEDGFAFYPACTNGHAVPTLFRLKGGAPVKKVAFGGDQVHEVAAVRSVTVEYNIHAVLDTLLASSSLRTFVVDKSLSIEEFADVVKEQVSDLL     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      MHSPDVI----VGDYVIISEKLFVRSKEEDGFAFYPACTNGHAVPTLFRLKGGAPVKKVAFGGDQVHEVAAVRSVTVEYNIHAVLDTLLASSSLRTFVVDKSLSIEEFADVVKEQVSDLL     
   consensus/100%                                               ..os-sl....VGs.VhIsthhhlc.K-p-tas..shssNhhsssshFpLKGuAPs.KVsFGsDpVhEVtuh+SVslpaplcthlDplLspps.t.asV-huhplpEFAsVVt-tV.chL     
   consensus/90%                                                QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC..ALAPNMMVTNNTFTLKGGAPT.KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA.YTVELGTEVNEFACVVADAVIKTL     
   consensus/80%                                                QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC..ALAPNMMVTNNTFTLKGGAPT.KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA.YTVELGTEVNEFACVVADAVIKTL     
   consensus/70%                                                QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC..ALAPNMMVTNNTFTLKGGAPT.KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA.YTVELGTEVNEFACVVADAVIKTL     

                                                cov    pid  961          .         .         .         0         .         .         .         .         :         .         .         . 1080
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      QPVSELLTPLGIDLDEWSIATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQLEEEQEE--DWLDDDSQQTVGQQDGSE     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQ-EEEQEE--DWLDDDSQQTVGQQDGSE     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      VKLLRGMPIPDFDLDDFIDAPCYCFNAEGDASWSSTMIFSLHPVECDEECSEVEASDLEEGESECISETSTEQVDVSHEVSDDEWAAAVDEAFPLDEAEDVTESVQEEAQPVEVPVEDIA     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      VKLLRGMPIPDFDLDDFIDAPCYCFNAEGDASWSSTMIFSLHPVECDEECSEVEASDLEEGESECISETSTEQVDVSHEVSDDEWAAAVDEAFPLDEAEDVTESVQEEAQPVEVPVEDIA     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      VKLLRGMPIPDFDLDDFIDAPCYCFNAEGDASWSSTMIFSLHPVECDEECSEVEASDLEEGESECISETSTEQVDVSHEISDDEWAAAVDEAFPLDEAEDVTESVQEEAQPVEVPVEDIA     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      VKLLRGMPIPDFDLDDFIDAPCYCFNAEGDASWSSTMIFSLHPVECDEECSEVEASDLEEGESECISETSTEQVDVSHEISDDEWAAAVDEAFPLDEAEDVTESVQEEAQPVEVPVEDIA     
   consensus/100%                                               ..l.chhs..shDLD-a..AshYhFstpG-hphuSpMhhShaPs-pDEEpu-sEtp-hE.upp....EhuTEp...saphps.EauAsssth...-EtE-..-.lp--uQ.s.s..-s.t     
   consensus/90%                                                QPVSELLTPLGIDLDEWShATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ...YEYGTED...DYQGKPLEFGATSAALQPEEEQEE..DWLDDDSQQTVGQQDGSE     
   consensus/80%                                                QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ...YEYGTED...DYQGKPLEFGATSAALQPEEEQEE..DWLDDDSQQTVGQQDGSE     
   consensus/70%                                                QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ...YEYGTED...DYQGKPLEFGATSAALQPEEEQEE..DWLDDDSQQTVGQQDGSE     

                                                cov    pid 1081          .         1         .         .         .         .         :         .         .         .         .         2 1200
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      QVVIADTLQETPVVSDTVEVPPQVVKLPSEPQTIQPEVKEVAPVYEADTEQTQSVTVKPKRLRKKRNVDPLSNFEHKVITECVTIVLGDAIQVAKCYGESVLVNAANTHLKHGGGIAGAI     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      QVVIADTLQETPVVSDTVEVPPQVVKLPSEPQTIQPEVKEVAPVYEADTEQTQSVTVKPKRLRKKRNVDPLSNFEHKVITECVTIVLGDAIQVAKCYGESVLVNAANTHLKHGGGIAGAI     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      QVVIADTLQETPVVSDTVEVPPQVVKLPSEPQTIQPEVKEVAPVYEADTEQTQSVTVKPKRLRIKRNVDPLSNFEHKVITECVTIVLGDAIQVAKCYGESVLVNAANTHLKHGGGIAGAI     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      QVVIADTLQETPVVSDTVEVPPQVVKLPSEPQTIQPEVKEVAPVYEADTEQTQSVTVKPKRLRIKRNVDPLSNFEHKVITECVTIVLGDAIQVAKCYGESVLVNAANTHLKHGGGIAGAI     
   consensus/100%                                               p.......ppTsslpshVEV.PQl........plpP.Vppl.........................pVsshSsa.+..lT-sVhIh.uDhlp.AKpht.oVlVNAANsaLKHGGGlAGAl     
   consensus/90%                                                D.......NQTTTIQTIVEVQPQL......EMELTPVVQTI.........................EVNSFSGYLK..LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
   consensus/80%                                                D.......NQTTTIQTIVEVQPQL......EMELTPVVQTI.........................EVNSFSGYLK..LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     
   consensus/70%                                                D.......NQTTTIQTIVEVQPQL......EMELTPVVQTI.........................EVNSFSGYLK..LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL     

                                                cov    pid 1201          .         .         .         .         :         .         .         .         .         3         .         . 1320
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      NKATNNAMQFESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      NAASKGAVQKESDEYILAKGPLQVGDSVLLQGHSLAKNILHVVGPDARAKQDVSLLSKCYKAMNAYPLVVTPLVSAGIFGVKPAVSFDYLIREAKTRVLVVVNSQDVYKSLT--------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      NAASKGAVQKESDEYILAKGPLQVGDSVLLQGHSLAKNILHVVGPDARAKQDVSLLSKCYKAMNAYPLVVTPLVSAGIFGVKPAVSFDYLIREAKTRVLVVVNSQDVYKSLT--------     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      NAASKGAVQKESDEYILAKGPLQVGDSVLLQGHSLAKNILHVVGPDARAKQDVSLLSKCYKAMNAYPLVVTPLVSAGIFGVKPAVSFDYLIREAKTRVLVVVNSQDVYKSLT--------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      NAASKGAVQKESDEYILAKGPLQVGDSVLLQGHSLAKNILHVVGPDARAKQDVSLLSKCYKAMNAYPLVVTPLVSAGIFGVKPAVSFDYLIREAKTRVLVVVNSQDVYKSLT--------     
   consensus/100%                                               NtAopsAhQhESD-YIhspGPLpVGsSslLpGHsLAKphLHVVGPsspttpDlpLLppsYcshNta.lllsPLlSAGIFGscPhhShchhlcps+TpVhlsV.spslYcpLs........     
   consensus/90%                                                NKATNNAMQhESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
   consensus/80%                                                NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     
   consensus/70%                                                NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS     

                                                cov    pid 1321          .         .         :         .         .         .         .         4         .         .         .         . 1440
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      -------IVDIPQ------------------------------------------------------------------SLTFS------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      -------IVDIPQ------------------------------------------------------------------SLTFS------------------------------------     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      -------IVDIPQ------------------------------------------------------------------SLTFS------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      -------IVDIPQ------------------------------------------------------------------SLTFS------------------------------------     
   consensus/100%                                               .......Is-IPp..................................................................slTF.....................................     
   consensus/90%                                                EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
   consensus/80%                                                EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     
   consensus/70%                                                EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK     

                                                cov    pid 1441          :         .         .         .         .         5         .         .         .         .         :         . 1560
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      -------------YDG-------------------------------------------LRGAIRKAKDYGFTVFVCTDNSANTKVLRNK--GVDYTKKFLTVDGVQYYCYTSKDTLDDI     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      -------------YDG-------------------------------------------LRGAIRKAKDYGFTVFVCTDNSANTKVLRNK--GVDYTKKFLTVDGVQYYCYTSKDTLDDI     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      -------------YDG-------------------------------------------LRGAIRKAKDYGFTVFVCTDNSANTKVLRNK--GVDYTKKFLTVDGVQYYCYTSKDTLDDI     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      -------------YDG-------------------------------------------LRGAIRKAKDYGFTVFVCTDNSANTKVLRNK--GVDYTKKFLTVDGVQYYCYTSKDTLDDI     
   consensus/100%                                               .............YsG...........................................LRthlt+Ac-hthhh.VCs-spA.spslppK..Glchpcthlsh.GspaYhYTSKsTlssl     
   consensus/90%                                                ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY.GARFYFYTSKTTVASL     
   consensus/80%                                                ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY.GARFYFYTSKTTVASL     
   consensus/70%                                                ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY.GARFYFYTSKTTVASL     

                                                cov    pid 1561          .         .         .         6         .         .         .         .         :         .         .         . 1680
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      LQQANK-SVGIISMPLGYVSHGLDLIQAGSVVRRVNVPYVCLLANKEQEAI---LMSEDVKLNPSEDFIKHVRTNGGYNSWHLVEGELLVQDLRLN-KLLHWSDQTICYKDSVFYVVKNS     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      LQQANK-SVGIISMPLGYVSHGLDLIQAGSVVRRVNVPYVCLLANKEQEAI---LMSEDVKLNPSEDFIKHVRTNGGYNSWHLVEGELLVQDLRLN-KLLHWSDQTICYKDSVFYVVKNS     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      LQQANK-SVGIISMPLGYVSHGLDLIQAGSVVRRVNVPYVCLLANKEQEAI---LMSEDVKLNPSEDFIKHVRTNGGYNSWHLVEGELLVQDLRLN-KLLHWSDQTICYKDSVFYVVKNS     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      LQQANK-SVGIISMPLGYVSHGLDLIQAGSVVRRVNVPYVCLLANKEQEAI---LMSEDVKLNPSEDFIKHVRTNGGYNSWHLVEGELLVQDLRLN-KLLHWSDQTICYKDSVFYVVKNS     
   consensus/100%                                               lpphNc.s.slloMPLGYVoHGLsL.pAuphhRplpVPhss.lus.-t.sh...hhopssK.sPpEcFIcplphsGuYpsWphst.....QshpLs.chL+huDpolhYpssshhhhhsu     
   consensus/90%                                                INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK.TPEEHFIETISLAGSYKDWSYSG.....QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
   consensus/80%                                                INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK.TPEEHFIETISLAGSYKDWSYSG.....QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     
   consensus/70%                                                INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK.TPEEHFIETISLAGSYKDWSYSG.....QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG     

                                                cov    pid 1681          .         7         .         .         .         .         :         .         .         .         .         8 1800
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      TAFPFETLSACRAYLDSRTTQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALK--ELYGPVDPTFLHRFYSLKAAVHKWKMVV     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      TAFPFETLSACRAYLDSRTTQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALK--ELYGPVDPTFLHRFYSLKAAVHKWKMVV     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      TAFPFETLSACRAYLDSRTTQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALK--ELYGPVDPTFLHRFYSLKAAVHKWKMVV     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      TAFPFETLSACRAYLDSRTTQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALK--ELYGPVDPTFLHRFYSLKAAVHKWKMVV     
   consensus/100%                                               pshsF-sL...+shLs.Rpsp..TIcVhsTVDslNh+T.Vls.p.TYtpQhGssahsGADlochhPcppppG+ohYl...LssD-Thtlc..EhYtssDPoFLtRahShhsts+KWKhs.     
   consensus/90%                                                EVITFDNL...KTLLSLREVR..TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV...LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
   consensus/80%                                                EVITFDNL...KTLLSLREVR..TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV...LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     
   consensus/70%                                                EVITFDNL...KTLLSLREVR..TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV...LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ     

                                                cov    pid 1801          .         .         .         .         :         .         .         .         .         9         .         . 1920
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHXNLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      CDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGSPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGLKACCYVGVQTVED     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      CDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGSPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGLKACCYVGVQTVED     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      CDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGAPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGLKACCYVGVQTVED     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      CDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGAPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGLKACCYVGVQTVED     
   consensus/100%                                               sstlpSlKhuDNNCYLssslhTLp.l.-lKFs.PALQcAah+t+uG-ussFhALIhAYsNpThGt.sDspchhphlht+.pLssstR.Vhp.hCpsCG.ppssLpGlcAshYhGs.ohEp     
   consensus/90%                                                VNGLTSIKWADNNCYLATALLTLQQI.ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR.VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
   consensus/80%                                                VNGLTSIKWADNNCYLATALLTLQQI.ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR.VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     
   consensus/70%                                                VNGLTSIKWADNNCYLATALLTLQQI.ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR.VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ     

                                                cov    pid 1921          .         .         :         .         .         .         .         0         .         .         .         . 2040
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      LRARMTYVCQCGGERHRQIVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSDCNVVRYSLDGNFRTEVD     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      LRARMTYVCQCGGERHRQIVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSDCNVVRYSLDGNFRTEVD     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      LRARMTYVCQCGGERHRQIVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSDCNVVRYSLDGNFRTEVD     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      LRARMTYVCQCGGERHRQIVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSDCNVVRYSLDGNFRTEVD     
   consensus/100%                                               h+tthphsCpCGtptp+.lVpppoPalhhSusPsph.lppuT...Fsshs.apG.phtsGHYhHhp.KtsL.hphDuuhloKoS-aKs.lTDVha.tppYooshpsVpYpLDGshpTElD     
   consensus/90%                                                FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT...FTCASEYTG.NYQCGHYKHITSKETL.YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
   consensus/80%                                                FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT...FTCASEYTG.NYQCGHYKHITSKETL.YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     
   consensus/70%                                                FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT...FTCASEYTG.NYQCGHYKHITSKETL.YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID     

                                                cov    pid 2041          :         .         .         .         .         1         .         .         .         .         :         . 2160
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      PDLSAFYVKDGKYFTSEPPVTYSPATILAGSVYTNSCLVSSDGQPGGDAISLSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILWVNKASYDTNLNKF     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      PDLSAFYVKDGKYFTSEPPVTYSPATILAGSVYTNSCLVSSDGQPGGDAISLSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILWVNKASYDTNLNKF     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      PDLSAFYVKDGKYFTSEPPVTYSPATILAGSVYTNSCLVSSDGQPGGDAISLSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILWVNKASYDTNLNKF     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      PDLSAFYVKDGKYFTSEPPVTYSPATILAGSVYTNSCLVSSDGQPGGDAISLSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILWVNKASYDTNLNKF     
   consensus/100%                                               PcLssaYhKDspYFT.E.PlshsPsp.hssusasN.phVssshp.usD.....hNpLhGac..KPso+chphoFhPc.sGDVlhh-acpYsP.aKpGAhhhtKPIlWhspsuhspsh.K.     
   consensus/90%                                                PKLDNYYKKDNSYFT.EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD.....LNQLTGYK..KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
   consensus/80%                                                PKLDNYYKKDNSYFT.EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD.....LNQLTGYK..KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     
   consensus/70%                                                PKLDNYYKKDNSYFT.EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD.....LNQLTGYK..KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP     

                                                cov    pid 2161          .         .         .         2         .         .         .         .         :         .         .         . 2280
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      NRASLRQIFDVAPIELENKFTPLSVEST------------PVEPPTVDVVALQQEMTIVKCKGLNKPFVKDNVSFVADDSGTPVVEYLSKEDLHTLYVDPKYQVIVLKDNVLSSMLRLHT     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      NRASLRQIFDVAPIELENKFTPLSVEST------------PVEPPTVDVVALQQEMTIVKCKGLNKPFVKDNVSFVADDSGTPVVEYLSKEDLHTLYVDPKYQVIVLKDNVLSSMLRLHT     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      NRASLRQIFDVAPIELENKFTPLSVEST------------PVEPPTVDVVALQQEMTIVKCKGLNKPFVKDNVSFVADDSGTPVVEYLSKEDLHTLYVDPKYQVIVLKDNVLSSMLRLHT     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      NRASLRQIFDVAPIELENKFTPLSVEST------------PVEPPTVDVVALQQEMTIVKCKGLNKPFVKDNVSFVADDSGTPVVEYLSKEDLHTLYVDPKYQVIVLKDNVLSSMLRLHT     
   consensus/100%                                               NphslRplasstPlEhpNpFssLpsEss............PVp..sV-ssslQp-..llcCpshsp.hVtD.l.hhssssuh.lsE.lu+pDLhshYVD.p.plhlhKsN.LSphLtL+T     
   consensus/90%                                                NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD..VLECNVKTTEVVGD.IILKPANNSLKITEEVGHTDLMAAYVD.NSSLTIKKPNELSRVLGLKT     
   consensus/80%                                                NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD..VLECNVKTTEVVGD.IILKPANNSLKITEEVGHTDLMAAYVD.NSSLTIKKPNELSRVLGLKT     
   consensus/70%                                                NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD..VLECNVKTTEVVGD.IILKPANNSLKITEEVGHTDLMAAYVD.NSSLTIKKPNELSRVLGLKT     

                                                cov    pid 2281          .         3         .         .         .         .         :         .         .         .         .         4 2400
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRITNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------C-------FTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------C-------FTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      VESGDINVVAASGSLTRKVKLLFRASFYFKEFATRTFTATTA-VGSCIKSVVRHLGVTKGILTGCFSFVKMLFMLPLAYFSDSKLGTTEVKVSALKTAGVVTGNVVKQCCTAAVDLSMDK     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      VESGDINVVAASGSLTRKVKLLFRASFYFKEFATRTFTATTA-VGSCIKSVVRHLGVTKGILTGCFSFVKMLFMLPLAYFSDSKLGTTEVKVSALKTAGVVTGNVVKQCCTAAVDLSMDK     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      VESGDINVVAASGSLTRKVKLLFRASFYFKEFATRTFTATTA-VGSCIKSVVRHLGVTKGILTGCFSFVKMLFMLPLAYFSDSKLGTTEVKVSALKTAGVVTGNVVKQCCTAAVDLSMDK     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      VESGDINVVAASGSLTRKVKLLFRASFYFKEFATRTFTATTA-VGSCIKSVVRHLGVTKGILTGCFSFVKMLFMLPLAYFSDSKLGTTEVKVSALKTAGVVTGNVVKQCCTAAVDLSMDK     
   consensus/100%                                               ltotslssVsuss..Thts........YhK.Fhs+shosTTs.VspClppV.............C.......FhL.Lthho.o+.ssoclKsSh.pT...lstNsVKpssphsl-hShsh     
   consensus/90%                                                LATHGLAAVNSVPWDTIAN........YAKPFLNKVVSTTTNIVTRCLNRV.............Chsah.hhFTLLLQLCTFTR.TNSRIKASMPTT...IAKNTVKSVGKFCLEASFNY     
   consensus/80%                                                LATHGLAAVNSVPWDTIAN........YAKPFLNKVVSTTTNIVTRCLNRV.............CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT...IAKNTVKSVGKFCLEASFNY     
   consensus/70%                                                LATHGLAAVNSVPWDTIAN........YAKPFLNKVVSTTTNIVTRCLNRV.............CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT...IAKNTVKSVGKFCLEASFNY     

                                                cov    pid 2401          .         .         .         .         :         .         .         .         .         5         .         . 2520
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      LRRVDWKSTLRLLL-MLCTTMVLLSSVYHLYVFNQVLSSDVMFEDAQGLKKFYKEVRAYLGISSACDGLASAY-RANSFDVPTFCANRSAMCNWCLISQDSITHYPALKMVQTHLSHYVL     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      LRRVDWKSTLRLLL-MLCTTMVLLSSVYHLYVFNQVLSSDVMFEDAQGLKKFYKEVRAYLGISSACDGLASAY-RANSFDVPTFCANRSAMCNWCLISQDSITHYPALKMVQTHLSHYVL     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      LRRVDWKSTLRLLL-MLCTTMVLLSSVYHLYVFNQVLSSDVMFEDAQGLKKFYKEVRAYLGISSACDGLASAY-RANSFDVPTFCANRSAMCNWCLISQDSITHYPALKMVQTHLSHYVL     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      LRRVDWKSTLRLLL-MLCTTMVLLSSVYHLYVFNQVLSSDVMFEDAQGLKKFYKEVRAYLGISSACDGLASAY-RANSFDVPTFCANRSAMCNWCLISQDSITHYPALKMVQTHLSHYVL     
   consensus/100%                                               L+pssapphlplll.hLhhohsLhS.lYphhshs.lhSs....................LGhsShCsGhtpuY.pusshslsTaCss.Sh.CshCL.u.DSlspYPuLchlQhplSpahh     
   consensus/90%                                                LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN....................LGMPSYCTGYREGYLNSTNVTIATYCTG.SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
   consensus/80%                                                LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN....................LGMPSYCTGYREGYLNSTNVTIATYCTG.SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     
   consensus/70%                                                LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN....................LGMPSYCTGYREGYLNSTNVTIATYCTG.SIPCSVCLSGLDSLDTYPSLETIQITISSFKW     

                                                cov    pid 2521          .         .         :         .         .         .         .         6         .         .         .         . 2640
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIMA-----PISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIMA-----PISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      NIDWLWFAFETGLAYMLYTSAFNWLLLAGTLHYFFAQTSIFVDWRSYNYAVSSAFWLFTHI----PMAGLVRMYNLLACLWLLRKFYQHVINGCKDTACLLCYKRNRLTRVEASTVVCGG     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      NIDWLWFAFETGLAYMLYTSAFNWLLLAGTLHYFFAQTSIFVDWRSYNYAVSSAFWLFTHI----PMAGLVRMYNLLACLWLLRKFYQHVINGCKDTACLLCYKRNRLTRVEASTVVCGG     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      NIDWLWFAFETGLAYMLYTSAFNWLLLAGTLHYFFAQTSIFVDWRSYNYAVSSAFWLFTHI----PMAGLVRMYNLLACLWLLRKFYQHVINGCKDTACLLCYKRNRLTRVEASTVVCGG     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      NIDWLWFAFETGLAYMLYTSAFNWLLLAGTLHYFFAQTSIFVDWRSYNYAVSSAFWLFTHI----PMAGLVRMYNLLACLWLLRKFYQHVINGCKDTACLLCYKRNRLTRVEASTVVCGG     
   consensus/100%                                               slshhhhshEhhLAYhLaTphF.hLhLAuhhphFFu.hulah..pSa......hhWLhht.....PhuuhVRMY.hhAshahlhK.Y.HVlsGCpsosChhCYKRNRhTRVEsoTlVsGs     
   consensus/90%                                                DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW......LMWLIhsl....PISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
   consensus/80%                                                DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW......LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     
   consensus/70%                                                DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW......LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV     

                                                cov    pid 2641          :         .         .         .         .         7         .         .         .         .         :         . 2760
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKVSLPINVIVFDGK     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      KRTFYITANGGISFCRRHNWNCVDCDTAGVGNTFICEEVANDLTTALRRPINATDRSHYYVDSVTVKETVVQFNYRRDGQPFYERFPLCAFTNLDKLKFKEVCKTTTGIPEYNFIIYDSS     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      KRTFYITANGGISFCRRHNWNCVDCDTAGVGNTFICEEVANDLTTALRRPINATDRSHYYVDSVTVKETVVQFNYRRDGQPFYERFPLCAFTNLDKLKFKEVCKTTTGIPEYNFIIYDSS     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      KRTFYITANGGISFCRRHNWNCVDCDTAGVGNTFICEEVANDLTTALRRPINATDRSHYYVDSVTVKETVVQFNYRRDGQPFYERFPLCAFTNLDKLKFKEVCKTTTGIPEYNFIIYDSS     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      KRTFYITANGGISFCRRHNWNCVDCDTAGVGNTFICEEVANDLTTALRRPINATDRSHYYVDSVTVKETVVQFNYRRDGQPFYERFPLCAFTNLDKLKFKEVCKTTTGIPEYNFIIYDSS     
   consensus/100%                                               +RoFYlhANGGhuFC+hHNWNCVsCDThssGsTFIs-EVApDLohth+RPINsTDpSpYhVDSVTVKpsslph.ac+sGQ.hYERasLstFsNLDpL+....spsTps...hNhIlaDup     
   consensus/90%                                                RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR....ANNTKGSLPINVIVFDGK     
   consensus/80%                                                RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR....ANNTKGSLPINVIVFDGK     
   consensus/70%                                                RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR....ANNTKGSLPINVIVFDGK     

                                                cov    pid 2761          .         .         .         8         .         .         .         .         :         .         .         . 2880
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      DRGQESLARSACVYYSQVLCKSILLVDSSLITSVGDSSEIATKMFDSFVNSFVSLYNVTRDKLEKLISTARDGVRRGDNFHSVLTTFIDAARGPAGVESDVETNEIVDSVQYAHKHDIQI     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      DRGQESLARSACVYYSQVLCKSILLVDSSLITSVGDSSEIATKMFDSFVNSFVSLYNVTRDKLEKLISTARDGVRRGDNFHSVLTTFIDAARGPAGVESDVETNEIVDSVQYAHKHDIQI     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      DRGQESLARSACVYYSQVLCKSILLVDSSLVTSVGDSSEIATKMFDSFVNSFVSLYNVTRDKLEKLISTARDGVRRGDNFHSVLTTFIDAARGPAGVESDVETNEIVDSVQYAHKHDIQI     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      DRGQESLARSACVYYSQVLCKSILLVDSSLVTSVGDSSEIATKMFDSFVNSFVSLYNVTRDKLEKLISTARDGVRRGDNFHSVLTTFIDAARGPAGVESDVETNEIVDSVQYAHKHDIQI     
   consensus/100%                                               s+spES.A+SAsVYYSQlhCpsILLlDpuLlosVGDSuElAsKMFDuaVNoFsShaNVsh-KLcpLluTAcstlt+ssshcsVLoTFIsAAR..uhV-SDVETp-lV-slphuHppDIpl     
   consensus/90%                                                SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR.QGFVDSDVETKDVVECLKLSHQSDIEV     
   consensus/80%                                                SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR.QGFVDSDVETKDVVECLKLSHQSDIEV     
   consensus/70%                                                SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR.QGFVDSDVETKDVVECLKLSHQSDIEV     

                                                cov    pid 2881          .         9         .         .         .         .         :         .         .         .         .         0 3000
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHSIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      TNESYNNYVPSYVKPDSVSTSDLGSLIDCNAASVNQIVLRNSNGACIWNAAAYMKLSDALKRQIRIACRKCNLAFRLTTSKLRANDNILSVRFTANKIVGGAPTWFNVLRDFTLKGYVLA     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      TNESYNNYVPSYVKPDSVSTSDLGSLIDCNAASVNQIVLRNSNGACIWNAAAYMKLSDALKRQIRIACRKCNLAFRLTTSKLRANDNILSVRFTANKIVGGAPTWFNVLRDFTLKGYVLA     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      TNESYNNYVPSYVKPDSVSTSDLGSLIDCNAASVNQIVLRNSNGACIWNAAAYMKLSDALKRQIRIACRKCNLAFRLTTSKLRANDNILSVRFTANKIVGGAPTWFNALRDFTLKGYVLA     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      TNESYNNYVPSYVKPDSVSTSDLGSLIDCNAASVNQIVLRNSNGACIWNAAAYMKLSDALKRQIRIACRKCNLAFRLTTSKLRANDNILSVRFTANKIVGGAPTWFNALRDFTLKGYVLA     
   consensus/100%                                               Ts-ShNNYh.oYsKs-shospDLGuhIDCsAtplNt.Vh+spshAhIWNstsaMpLS-tL++QIR.As+KsNLsF+LTsuphRtssNllos+hs...lhGG.....phlpsa.LKthlhs     
   consensus/90%                                                TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA...LKGG.....KIVNNW.LKQLIKV     
   consensus/80%                                                TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA...LKGG.....KIVNNW.LKQLIKV     
   consensus/70%                                                TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA...LKGG.....KIVNNW.LKQLIKV     

                                                cov    pid 3001          .         .         .         .         :         .         .         .         .         1         .         . 3120
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      TIIVFLCAVLMYLCLPTFSMVPVEFYEDRILDFKVLDNGIIRDVNPDDKCFANKHRSFTQWYHEHVGGVYDNSITCPLTVAVIAGVAGARIPDVP-TTLAWVNNQIIFFVSRVFANTGSV     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      TIIVFLCAVLMYLCLPTFSMVPVEFYEDRILDFKVLDNGIIRDVNPDDKCFANKHRSFTQWYHEHVGGVYDNSITCPLTVAVIAGVAGARIPDVP-TTLAWVNNQIIFFVSRVFANTGSV     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      TIIVFLCAVLMYLCLPTFSMVPVEFYEDRILDFKVLDNGIIRDVNPDDKCFANKHRSFTQWYHEHVGGVYDNSITCPLTVAVIAGVAGARIPDVP-TTLAWVNNQIIFFVSRVFANTGSV     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      TIIVFLCAVLMYLCLPTFSMVPVEFYEDRILDFKVLDNGIIRDVNPDDKCFANKHRSFTQWYHEHVGGVYDNSITCPLTVAVIAGVAGARIPDVP-TTLAWVNNQIIFFVSRVFANTGSV     
   consensus/100%                                               TllhhhsAslhYLhhPsasMs.hp.apscIlsaKslDsGlhRDlsssDpCFANKHtsFspWapp+.GGsYsNshsCPLhsAVIst.sGhhlPslP.ThLthsNsphlaFlsRVFussGsl     
   consensus/90%                                                TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR.GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
   consensus/80%                                                TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR.GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     
   consensus/70%                                                TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR.GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI     

                                                cov    pid 3121          .         .         :         .         .         .         .         2         .         .         .         . 3240
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      CYTPSKLIEYTDIATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      CYTPIDEIPYKSFSDSGCILPSECTMFRDAEGRMTPYCHDPTVLPGAFAYSQMRPHVRYDLYDGNMFIKFPEVVFESTLRITRTLSTQYCRFGSCEYAQEGVCITTNGSWAIFNDHHLNR     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      CYTPIDEIPYKSFSDSGCILPSECTMFRDAEGRMTPYCHDPTVLPGAFAYSQMRPHVRYDLYDGNMFIKFPEVVFESTLRITRTLSTQYCRFGSCEYAQEGVCITTNGSWAIFNDHHLNR     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      CYTPIDEIPYKSFSDSGCILPSECTMFRDAEGRMTPYCHDPTVLPGAFAYSQMRPHVRYDLYDGNMFIKFPEVVFESTLRITRTLSTQYCRFGSCEYAQEGVCITTNGSWAIFNDHHLNR     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      CYTPIDEIPYKSFSDSGCILPSECTMFRDAEGRMTPYCHDPTVLPGAFAYSQMRPHVRYDLYDGNMFIKFPEVVFESTLRITRTLSTQYCRFGSCEYAQEGVCITTNGSWAIFNDHHLNR     
   consensus/100%                                               CYTP.c.I.YpshusSuClLsuECThF+DApG+.sPYCaDssVL.GuhAYpphRPcsRYsLhDGsh.IpFPpshhEuolRlspThsopYCRaGoCEhuptGVCloTsGpWsl.NDaahsh     
   consensus/90%                                                CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI.IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
   consensus/80%                                                CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI.IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     
   consensus/70%                                                CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI.IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL     

                                                cov    pid 3241          :         .         .         .         .         3         .         .         .         .         :         . 3360
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSYVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYLFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      PGVYCGSDFIDIVRRLAVSLFQPITYFQLTTSLVLGIGLCAFLTLLFYYINKVKRAFADYTQCAVIAVVAAVLNSLCICFVASIPLCIVPYTALYYYATFYFTNEPAFIMHVSWYIMFGP     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      PGVYCGSDFIDIVRRLAVSLFQPITYFQLTTSLVLGIGLCAFLTLLFYYINKVKRAFADYTQCAVIAVVAAVLNSLCICFVASIPLCIVPYTALYYYATFYFTNEPAFIMHVSWYIMFGP     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      PGVYCGSDFIDIVRRLAVSLFQPITYFQLTTSLVLGIGLCAFLTLLFYYINKVKRAFADYTQCAVIAVVAAVLNSLCICFVASIPLCIVPYTALYYYATFYFTNEPAFIMHVSWYIMFGP     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      PGVYCGSDFIDIVRRLAVSLFQPITYFQLTTSLVLGIGLCAFLTLLFYYINKVKRAFADYTQCAVIAVVAAVLNSLCICFVASIPLCIVPYTALYYYATFYFTNEPAFIMHVSWYIMFGP     
   consensus/100%                                               PGVaCGsDhlsllpphhssLhQPIshhplosSlVhGhhlshhlThLhYYh.+h+RAFu-Yo.ssshsslhhlhs.hslChsssh.hh.ssYoslYhYhTFYhTN-suFlhHlpWhlMFsP     
   consensus/90%                                                PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSaVVAFNTLLFLMSFTVLCLTPVYsFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
   consensus/80%                                                PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     
   consensus/70%                                                PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP     

                                                cov    pid 3361          .         .         .         4         .         .         .         .         :         .         .         . 3480
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGVMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      IVPIWMTCVYTVAMCFRHFFWVLAYFSKKHVEVFTDGKLNCSFQDAASNIFVINKDTYAALRNS--LTNDAYSRFLGLFNKYKYFSGAMETAAYREAAACHLAKALQTYSETGSDLLYQP     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      IVPIWMTCVYTVAMCFRHFFWVLAYFSKKHVEVFTDGKLNCSFQDAASNIFVINKDTYAALRNS--LTNDAYSRFLGLFNKYKYFSGAMETAAYREAAACHLAKALQTYSETGSDLLYQP     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      IVPIWMTCVYTVAMCFRHFFWVLAYFSKKHVEVFTDGKLNCSFQDAASNIFVINKDTYAALRNS--LTNDAYSRFLGLFNKYKYFSGAMETAAYREAAACHLAKALQTYSETGSDLLYQP     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      IVPIWMTCVYTVAMCFRHFFWVLAYFSKKHVEVFTDGKLNCSFQDAASNIFVINKDTYAALRNS--LTNDAYSRFLGLFNKYKYFSGAMETAAYREAAACHLAKALQTYSETGSDLLYQP     
   consensus/100%                                               lVPhWhThsYhlshsh+HFaWhhu.a.K++V.VF.sGh..soFp-AA.shFllNK-hYhtLRss..Ls.stYsRaLuLaNKYKYFSGsM-TsuYREAAsCHLAKALpsaSpoGSDlLYQP     
   consensus/90%                                                LVPFWITIAYIICISTKHFYWFFSNYLKRRV.VF.NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
   consensus/80%                                                LVPFWITIAYIICISTKHFYWFFSNYLKRRV.VF.NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     
   consensus/70%                                                LVPFWITIAYIICISTKHFYWFFSNYLKRRV.VF.NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP     

                                                cov    pid 3481          .         5         .         .         .         .         :         .         .         .         .         6 3600
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      PNCSITSGVLQSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVANPSTPAYTFTTV     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      PNCSITSGVLQSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVANPSTPAYTFTTV     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      PNCSITSGVLQSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVANPSTPAYTFTTV     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      PNCSITSGVLQSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVANPSTPAYTFTTV     
   consensus/100%                                               PpsSITSuVLQSGhhKMuaPSGcVEuCMVQVTCGohTLNGLWLDssVaCPRHVhCsu-ph.sPNY-sLLIphoNHsF.VQ...uusspLRVlGHuMQsslLKLpVDsANPpTPtYpFspl     
   consensus/90%                                                PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ...AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
   consensus/80%                                                PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ...AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     
   consensus/70%                                                PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ...AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI     

                                                cov    pid 3601          .         .         .         .         :         .         .         .         .         7         .         . 3720
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      KPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVAWLYAAILNGCAWFVKPNRTS     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      KPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVAWLYAAILNGCAWFVKPNRTS     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      KPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVAWLYAAILNGCAWFVKPNRTS     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      KPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVAWLYAAILNGCAWFVKPNRTS     
   consensus/100%                                               pPGtsFSVLACYNGpPoGsapssMRPNaTIKGSFLsGSCGSVGash-hsslsFCYMHpMELssGsHsGosh-GshYGsFhD+QstQsthTDphhoVNVlAWLYAAllNGstWFlp..pTo     
   consensus/90%                                                QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
   consensus/80%                                                QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     
   consensus/70%                                                QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT     

                                                cov    pid 3721          .         .         :         .         .         .         .         8         .         .         .         . 3840
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFFYE     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFFYE     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFFYE     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFFYE     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFFYE     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      VVSFNEWALANQFTEFVGTQSVDM---LAVKTGVAIEQLLYAIQQLY-TGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQSGVRKVTYGTAHWLFATLVSTYVIILQATKFTLWNYLFE     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      VVSFNEWALANQFTEFVGTQSVDM---LAVKTGVAIEQLLYAIQQLY-TGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQSGVRKVTYGTAHWLFATLVSTYVIILQATKFTLWNYLFE     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      VVSFNEWALANQFTEFVGTQSVDM---LAVKTGVAIEQLLYAIQQLY-TGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQSGVRKVTYGTAHWLFATLVSTYVIILQATKFTLWNYLFE     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      VVSFNEWALANQFTEFVGTQSVDM---LAVKTGVAIEQLLYAIQQLY-TGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQSGVRKVTYGTAHWLFATLVSTYVIILQATKFTLWNYLFE     
   consensus/100%                                               lssFN.hAht.pa.E.lspppVDh...LuspTGlAl.phhhulppLh.sGhpG+pILGSshLEDEFTP.DVshQh.GVshQSuV++shhGTtHWLhhTlloohllllQuTpaoLa.ahaE     
   consensus/90%                                                LNDFNLVAMKYNY.EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFhYE     
   consensus/80%                                                LNDFNLVAMKYNY.EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     
   consensus/70%                                                LNDFNLVAMKYNY.EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE     

                                                cov    pid 3841          :         .         .         .         .         9         .         .         .         .         :         . 3960
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      TIPTQLFPLLFVTMAFVMLLVKHKHTFLTLFLLPVAICLTYANIVYEPTTPISSALIAVANWLAPTNAYMRTTH-TDIGVYISMSLVLVIVVKRLYNPSLSNFALALCSGVMWLYTYSIG     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      TIPTQLFPLLFVTMAFVMLLVKHKHTFLTLFLLPVAICLTYANIVYEPTTPISSALIAVANWLAPTNAYMRTTH-TDIGVYISMSLVLVIVVKRLYNPSLSNFALALCSGVMWLYTYSIG     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      TIPTQLFPLLFVTMAFVMLLVKHKHTFLTLFLLPVAICLTYANIVYEPTTPISSALIAVANWLAPTNAYMRTTH-TDIGVYISMSLVLVIVVKRLYNPSLSNFALALCSGVMWLYTYSIG     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      TIPTQLFPLLFVTMAFVMLLVKHKHTFLTLFLLPVAICLTYANIVYEPTTPISSALIAVANWLAPTNAYMRTTH-TDIGVYISMSLVLVIVVKRLYNPSLSNFALALCSGVMWLYTYSIG     
   consensus/100%                                               sh.h.hh.hlhsh.AFsMhhVKHKHsFLsLFLLPshhslsYhNhVY.Pso.l....htlhsWLs.sss.hpsh+.pDhshYhShsllLllhstRhh.sshuphshsLhsslhhlYph.hG     
   consensus/90%                                                NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV....MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
   consensus/80%                                                NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV....MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     
   consensus/70%                                                NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV....MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG     

                                                cov    pid 3961          .         .         .         0         .         .         .         .         :         .         .         . 4080
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      EA-SSPIAYLVFVTTLTSDYTITVFVTVNLAKVCTYAIFAYSPQLTLVFPEVKMILLLYTCLGFMCTCYFGVFSLLNLKLRAPMGVYDFKVSTQEFRFMTANNLTAPRNSWEAMALNFKL     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      EA-SSPIAYLVFVTTLTSDYTITVFVTVNLAKVCTYAIFAYSPQLTLVFPEVKMILLLYTCLGFMCTCYFGVFSLLNLKLRAPMGVYDFKVSTQEFRFMTANNLTAPRNSWEAMALNFKL     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      EA-SSPIAYLVFVTTLTSDYTITVFVTVNLAKVCTYAIFAYSPQLTLVFPEVKMILLLYTCLGFMCTCYFGVFSLLNLKLRAPMGVYDFKVSTQEFRFMTANNLTAPRNSWEAMALNFKL     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      EA-SSPIAYLVFVTTLTSDYTITVFVTVNLAKVCTYAIFAYSPQLTLVFPEVKMILLLYTCLGFMCTCYFGVFSLLNLKLRAPMGVYDFKVSTQEFRFMTANNLTAPRNSWEAMALNFKL     
   consensus/100%                                               pA.spsIuhhshlholTSsYohsVhssh.LA+shsahhhtYsP.hhlshsplphIhLlYshLGahCTCYFGlFsLLNhhhRhshGVYDahVSTQEFRaMsupsLhsP+NSh-AhtLNhKL     
   consensus/90%                                                NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
   consensus/80%                                                NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     
   consensus/70%                                                NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL     

                                                cov    pid 4081          .         1         .         .         .         .         :         .         .         .         .         2 4200
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      IGIGGTPCIKVAAMQSKLTDLKCTSVVLLSVLQQLHLEANSRAWAFCVKCHNDILAATDPSEAFEKFVSLFATLMTFSGNVDLDALASDIFDTPSVLQATLSEFSHLATFAELEAAQKAY     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      IGIGGTPCIKVAAMQSKLTDLKCTSVVLLSVLQQLHLEANSRAWAFCVKCHNDILAATDPSEAFEKFVSLFATLMTFSGNVDLDALASDIFDTPSVLQATLSEFSHLATFAELEAAQKAY     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      IGIGGTPCIKVAAMQSKLTDLKCTSVVLLSVLQQLHLEANSRAWAFCVKCHNDILAATDPSEAFEKFVSLFATLMTFSGNVDLDALASDIFDTPSVLQATLSEFSHLATFAELEAAQKAY     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      IGIGGTPCIKVAAMQSKLTDLKCTSVVLLSVLQQLHLEANSRAWAFCVKCHNDILAATDPSEAFEKFVSLFATLMTFSGNVDLDALASDIFDTPSVLQATLSEFSHLATFAELEAAQKAY     
   consensus/100%                                               lGlGGpPCIKVAshQSKhoDlKCTSVVLLSVLQQL+lEusS+hWA.CVphHNDILhApDsoEAFEKhVSLhusLhohpGsVDlstLsp-hhDs.usLQAhhSEFSpLsoaAthtsAQcAY     
   consensus/90%                                                LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
   consensus/80%                                                LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     
   consensus/70%                                                LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY     

                                                cov    pid 4201          .         .         .         .         :         .         .         .         .         3         .         . 4320
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      QEAMDSGDTSPQVLKALQKAVNIAKNAYEKDKAVARKLERMADQAMTSMYKQARAEDKKAKIVSAMQTMLFGMIKKLDNDVLNGIISNARNGCIPLSVIPLCASNKLRVVIPDFTVWNQV     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      QEAMDSGDTSPQVLKALQKAVNIAKNAYEKDKAVARKLERMADQAMTSMYKQARAEDKKAKIVSAMQTMLFGMIKKLDNDVLNGIISNARNGCIPLSVIPLCASNKLRVVIPDFTVWNQV     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      QEAMDSGDTSPQVLKALQKAVNIAKNAYEKDKAVARKLERMADQAMTSMYKQARAEDKKAKIVSAMQTMLFGMIKKLDNDVLNGIISNARNGCIPLSVIPLCASNKLRVVIPDFTVWNQV     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      QEAMDSGDTSPQVLKALQKAVNIAKNAYEKDKAVARKLERMADQAMTSMYKQARAEDKKAKIVSAMQTMLFGMIKKLDNDVLNGIISNARNGCIPLSVIPLCASNKLRVVIPDFTVWNQV     
   consensus/100%                                               ppAhssGD.S..VLKtLpKulNlAKsta-+DtAhtRKLE+MADQAMTpMYKQARuEDK+AKlsSAMQTMLFsMl+KLDNDsLNsIIsNARsGClPLslIPLssusKLhVVIPDassapps     
   consensus/90%                                                EQAVANGD.SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
   consensus/80%                                                EQAVANGD.SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     
   consensus/70%                                                EQAVANGD.SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT     

                                                cov    pid 4321          .         .         :         .         .         .         .         4         .         .         .         . 4440
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      CDGTTFIYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      VTYPSLNYAGALWDITVINNVDNEIVKSSDV-VDSNENLTWPLVLECTRASTSAVKLQNNEIKPSGLKTMVVSAGQEQTNC-NTSSLAYYEPVQGRKMLMALLSDNAYLKWARVEGKD--     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      VTYPSLNYAGALWDITVINNVDNEIVKSSDV-VDSNENLTWPLVLECTRASTSAVKLQNNEIKPSGLKTMVVSAGQEQTNC-NTSSLAYYEPVQGRKMLMALLSDNAYLKWARVEGKD--     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      VTYPSLNYAGALWDITVINNVDNEIVKSSDV-VDSNENLTWPLVLECTRASTSAVKLQNNEIKPSGLKTMVVSAGQEQTNC-NTSSLAYYEPVQGRKMLMALLSDNAYLKWARVEGKD--     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      VTYPSLNYAGALWDITVINNVDNEIVKSSDV-VDSNENLTWPLVLECTRASTSAVKLQNNEIKPSGLKTMVVSAGQEQTNC-NTSSLAYYEPVQGRKMLMALLSDNAYLKWARVEGKD--     
   consensus/100%                                               sshsoh.YAuALW-Ip.lsssDscIVp.S-l.hDss.NLsWPLllpshRAs.SAVKLQNNElpPsuL+pMssuAGppQTsC.sssuLAYYpsspGt+hlhALLSD.t.LKWARh.tpD..     
   consensus/90%                                                CDGTTFsYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN.SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
   consensus/80%                                                CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN.SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     
   consensus/70%                                                CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN.SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT     

                                                cov    pid 4441          :         .         .         .         .         5         .         .         .         .         :         . 4560
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESLG     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      GFVSVELQPPCKFLIAGPKGPEIRYLYFVKNLNNLHRGQVLGHIAATVRLQAGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKTGTGIAISVKPESTADQETYG     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      GFVSVELQPPCKFLIAGPKGPEIRYLYFVKNLNNLHRGQVLGHIAATVRLQAGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKTGTGIAISVKPESTADQETYG     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      GFVSVELQPPCKFLIAGPKGPEIRYLYFVKNLNNLHRGQVLGHIAATVRLQAGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKTGTGIAISVKPESTADQETYG     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      GFVSVELQPPCKFLIAGPKGPEIRYLYFVKNLNNLHRGQVLGHIAATVRLQAGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKTGTGIAISVKPESTADQETYG     
   consensus/100%                                               Ghl.sELpPPC+FlhssPKGPcl+YLYFlKsLNNLpRG.VLGplAATVRLQAGssTEhsuNSoVLShssFsVDstKAYhDalsuGGtPlTNCVKMLss+TGTG.AIoVpPEushDQEohG     
   consensus/90%                                                GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESaG     
   consensus/80%                                                GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     
   consensus/70%                                                GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG     

                                                cov    pid 4561          .         .         .         6         .         .         .         .         :         .         .         . 4680
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLN-----------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLN-----------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      GASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVCQYWIGYGCNCDSLRQAALPQSKDSNFL------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      GASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVCQYWIGYGCNCDSLRQAALPQSKDSNFLNRVRGSIVNARIEPCSSGLSTDVVFRAFDICNYKAKVAGIGK     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      GASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVCQYWIGYGCNCDSLRQAALPQSKDSNFL------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      GASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVCQYWIGYGCNCDSLRQAALPQSKDSNFLKRVRGSIVNARIEPCSSGLSTDVVFRAFDICNYKAKVAGIGK     
   consensus/100%                                               GASsCLYCRsHI-HPsspGhCchKGKaVQIPspCspDPVGFsLpNTsCsVCthWhGYGCsCDpLRpshL.pucspsFL..........................................     
   consensus/90%                                                GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVpG.lssARlpPCuoGhSTDVVaRAFDI..YpsKVAGhuK     
   consensus/80%                                                GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG.VSAARLTPCGTGTSTDVVYRAFDI..YNDKVAGFAK     
   consensus/70%                                                GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG.VSAARLTPCGTGTSTDVVYRAFDI..YNDKVAGFAK     

                                                cov    pid 4681          .         7         .         .         .         .         :         .         .         .         .         8 4800
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      YYKTNTCRFVELDDQGHHLDSYFVVKRHTMENYELEKHCYDLLRDCDAVAPHDFFIFDVDKVKTPHIVRQRLTEYTMMDLVYALRHFDQ-NSEVLKAILVKYGCCDVTYFENKLWFDFVE     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      YYKTNTCRFVELDDQGHHLDSYFVVKRHTMENYELEKHCYDLLRDCDAVAPHDFFIFDVDKVKTPHIVRQRLTEYTMMDLVYALRHFDQ-NSEVLKAILVKYGCCDVTYFENKLWFDFVE     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                ahKTNsCRF.EhD-psphlDSYFVVKRHThpNYphEcphYsLL+DCsAVA.HDFFhFclDtshsPHIsRQRLTcYTMhDLVYALRHFDp.Ns-sLKtILVpYsCCDssYFppK.WaDFVE     
   consensus/80%                                                FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     
   consensus/70%                                                FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE     

                                                cov    pid 4801          .         .         .         .         :         .         .         .         .         9         .         . 4920
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      NPSVIGVYHKLGERVRQAILNTVKFCDHMVKAGLVGVLTLDNQDLNGKWYDFGDFVITQPGSGVAIVDSYYSYLMPVLSMTDCLAAETHRDCDFNKPLIEWPLTEYDFTDYKVQLFEKYF     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      NPSVIGVYHKLGERVRQAILNTVKFCDHMVKAGLVGVLTLDNQDLNGKWYDFGDFVITQPGSGVAIVDSYYSYLMPVLSMTDCLAAETHRDCDFNKPLIEWPLTEYDFTDYKVQLFEKYF     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                NPslltVYtpLGERVRQAlLpTVpFCDtMhpAGlVGVLTLDNQDLNGpWYDFGDFl.TpPGSGVslVDSYYShLMPlLohTcsLsAEoHhDsDhsKPhIcWsLhcYDFT-.+lpLF-+YF     
   consensus/80%                                                NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     
   consensus/70%                                                NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF     

                                                cov    pid 4921          .         .         :         .         .         .         .         0         .         .         .         . 5040
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      KYWDQTYHANCVNCTDDRCVLHCANFNVLFAMTMPKTCFGPIVRKIFVDGVPFVVSCGYHYKELGLVMNMDVSLHRHRLSLKELMMYAADPAMHIASSNAFLDLRTSCFSVAALTTGLTF     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      KYWDQTYHANCVNCTDDRCVLHCANFNVLFAMTMPKTCFGPIVRKIFVDGVPFVVSCGYHYKELGLVMNMDVSLHRHRLSLKELMMYAADPAMHIASSNAFLDLRTSCFSVAALTTGLTF     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                KYWDQTYHsNCVNChDDRClLHCANFNVLFuhshP.TsFGPlVRKIFVDGVPFVVSsGYHa+ELGlVhN.DVsLHppRLShKELhhYAADPAMHhASuNhhLDhRToCFSVAALTsslsF     
   consensus/80%                                                KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     
   consensus/70%                                                KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF     

                                                cov    pid 5041          :         .         .         .         .         1         .         .         .         .         :         . 5160
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      QTVRPGNFNQDFYDFVVSKGFFKEGSSVTLKHFFFAQDGNAAITDYNYYSYNLPTMCDIKQMLFCMEVVNKYFEIYDGGCLNASEVVVNNLDKSAGHPFNKFGKARVYYESMSYQEQDEL     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      QTVRPGNFNQDFYDFVVSKGFFKEGSSVTLKHFFFAQDGNAAITDYNYYSYNLPTMCDIKQMLFCMEVVNKYFEIYDGGCLNASEVVVNNLDKSAGHPFNKFGKARVYYESMSYQEQDEL     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                QTV+PGNFNpDFYDFsVSKGFFKEGSSVpLKHFFFAQDGNAAIoDYsYYpYNLPTMCDI+QhLFshEVVsKYF-hYDGGClNAspVlVNNLDKSAGaPFNKaGKARlYY-SMSYp-QDtL     
   consensus/80%                                                QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     
   consensus/70%                                                QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL     

                                                cov    pid 5161          .         .         .         2         .         .         .         .         :         .         .         . 5280
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      FAMTKRNVIPTMTQMNLKYAISAKNRARTVAGVSILSTMTNRQYHQKMLKSMAATRGATCVIGTTKFYGGWDFMLKTLYKDVDNPHLMGWDYPKCDRAMPNMCRIFASLILARKHGTCCT     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      FAMTKRNVIPTMTQMNLKYAISAKNRARTVAGVSILSTMTNRQYHQKMLKSMAATRGATCVIGTTKFYGGWDFMLKTLYKDVDNPHLMGWDYPKCDRAMPNMCRIFASLILARKHGTCCT     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                FAhTKRNVIPThTQMNLKYAISAKNRARTVAGVSIhSTMTNRQaHQKhLKShAATRGATsVIGToKFYGGWc.MLKTlYpDV-NPHLMGWDYPKCDRAMPNMhRIhASLlLARKHsTCCo     
   consensus/80%                                                FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     
   consensus/70%                                                FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS     

                                                cov    pid 5281          .         3         .         .         .         .         :         .         .         .         .         4 5400
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      TRDRFYRLANECAQVLSEYVLCGGGYYVKPGGTSSGDATTAYANSVFNILQATTANVSALMGANGNKIVDKEVKDMQFDLYVNVYRSTSPDPKFVDKYYAFLNKHFSMMILSDDGVVCYN     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      TRDRFYRLANECAQVLSEYVLCGGGYYVKPGGTSSGDATTAYANSVFNILQATTANVSALMGANGNKIVDKEVKDMQFDLYVNVYRSTSPDPKFVDKYYAFLNKHFSMMILSDDGVVCYN     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                hpcRFYRLANECAQVLSEhVhCGGuhYVKPGGTSSGDATTAYANSVFNIhQAsTANVsALhussGNKIsDK.V+shQacLY.slYRspssDscFVscaYAaLpKHFSMMILSDDuVVCaN     
   consensus/80%                                                LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     
   consensus/70%                                                LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN     

                                                cov    pid 5401          .         .         .         .         :         .         .         .         .         5         .         . 5520
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      SDYAAKGYIAGIQNFKETLYYQNNVFMSEAKCWVETDLKKGPHEFCSQHTLYIKDGDDGYFLPYPDPSRILSAGCFVDDIVKTDGTLMVERFVSLAIDAYPLTKHEDIEYQNVFWVYLQY     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      SDYAAKGYIAGIQNFKETLYYQNNVFMSEAKCWVETDLKKGPHEFCSQHTLYIKDGDDGYFLPYPDPSRILSAGCFVDDIVKTDGTLMVERFVSLAIDAYPLTKHEDIEYQNVFWVYLQY     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                SsYAupGhlAuIpNFKpsLYYQNNVFMSEAKCWsETDLpKGPHEFCSQHThhlKpGDDhhaLPYPDPSRILuAGCFVDDIVKTDGTLMlERFVSLAIDAYPLTKH.s.EYtsVFalYLQY     
   consensus/80%                                                STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     
   consensus/70%                                                STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY     

                                                cov    pid 5521          .         .         :         .         .         .         .         6         .         .         .         . 5640
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      IEKLYKDLTGHMLDSYSVMLCGDNSAKFWEEAFYRDLYSSPTTLQAVGSCVVCHSQTSLRCGTCIRRPFLCCKCCYDHVIATPHKMVLSVSPYVCNAPGCGVSDVTKLYLGGMSYFCVDH     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      IEKLYKDLTGHMLDSYSVMLCGDNSAKFWEEAFYRDLYSSPTTLQAVGSCVVCHSQTSLRCGTCIRRPFLCCKCCYDHVIATPHKMVLSVSPYVCNAPGCGVSDVTKLYLGGMSYFCVDH     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                IcKLac-LTGHMLD.YSVMLssDNou+aWE.tFYcshYos.TsLQAVGuCVlCpSQTSLRCGsCIRRPFLCCKCCYDHVIuTsHKhVLSVsPYVCNAPGCsVoDVTpLYLGGMSYaChsH     
   consensus/80%                                                IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     
   consensus/70%                                                IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH     

                                                cov    pid 5641          :         .         .         .         .         7         .         .         .         .         :         . 5760
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      RPVCSFPLCANGLVFGLYKNMCTGSPSIVEFNRLATCDWTESGDYTLANTTTEPLKLFAAETLRATEEASKQSYAIATIKEIVGERQLLLVWEAGKSKPPLNRNYVFTGYHITKNSKVQL     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      RPVCSFPLCANGLVFGLYKNMCTGSPSIVEFNRLATCDWTESGDYTLANTTTEPLKLFAAETLRATEEASKQSYAIATIKEIVGERQLLLVWEAGKSKPPLNRNYVFTGYHITKNSKVQL     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                +PshSFPLCANG.VFGLYKNhCsGSssls-FNtlATCDWTpuGDYhLANTsTE.LKLFAAETL+ATEEs.K.SYuIATl+Ellu-RpLhLsWEsGKs+PPLNRNYVFTGY+lTKNSKVQl     
   consensus/80%                                                KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     
   consensus/70%                                                KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI     

                                                cov    pid 5761          .         .         .         8         .         .         .         .         :         .         .         . 5880
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPILNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      GEYIFERIDYSDAVSYKSSTTYKLTVGDIFVLTSHSVATLTAPTIVNQERYVKITGLYPTITVPEEFASHVANFQKSGYSKYVTVQGPPGTGKSHFAIGLAIYYPTARVVYTACSHAAVD     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      GEYIFERIDYSDAVSYKSSTTYKLTVGDIFVLTSHSVATLTAPTIVNQERYVKITGLYPTITVPEEFASHVANFQKSGYSKYVTVQGPPGTGKSHFAIGLAIYYPTARVVYTACSHAAVD     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                GEYhFE+hDYuDAVsY+uoTTYKLsVGDhFVLTSHoVhsLoAPTlVsQE+YV+ITGLYPhlsls-EFuSpVANaQKsGhpKYsTlQGPPGTGKSHFAIGLAlYYPoARlVYTACSHAAVD     
   consensus/80%                                                GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     
   consensus/70%                                                GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD     

                                                cov    pid 5881          .         9         .         .         .         .         :         .         .         .         .         0 6000
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHCVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      ALCEKAFKYLNIAKCSRIIPAKARVECYDRFKVNETNSQYLFSTINALPETSADILVVDEVSMCTNYDLSIINARIKAKHIVYVGDPAQLPAPRTLLTRGTLEPENFNSVTRLMCNLGPD     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      ALCEKAFKYLNIAKCSRIIPAKARVECYDRFKVNETNSQYLFSTINALPETSADILVVDEVSMCTNYDLSIINARIKAKHIVYVGDPAQLPAPRTLLTRGTLEPENFNSVTRLMCNLGPD     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                ALCEKAhKYLsIsKCSRIIPA+ARVECaD+FKVNpT.pQYlFsTlNALPEToADIlVhDElSMsTNYDLSllNARl+AKHhVYlGDPAQLPAPRTLLT+GTLEPE.FNSVsRLMpslGPD     
   consensus/80%                                                ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     
   consensus/70%                                                ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD     

                                                cov    pid 6001          .         .         .         .         :         .         .         .         .         1         .         . 6120
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      IFLSMCYRCPKEIVSTVSALVYNNKLLAKKELSGQCFKILYKGNVTHDASSAINRPQLTFVKNFITANPAWSKAVFISPYNSQNAVARSMLGLTTQTVDSSQGSEYQYVIFCQTADTAHA     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      IFLSMCYRCPKEIVSTVSALVYNNKLLAKKELSGQCFKILYKGNVTHDASSAINRPQLTFVKNFITANPAWSKAVFISPYNSQNAVARSMLGLTTQTVDSSQGSEYQYVIFCQTADTAHA     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                hFLuhChRCPtEIVsTVSALVYsNKLhA+K-hSuQCFKhhYKGslTHDsSSAINRPQlshV+pFlTtNPAWpKAVFISPYNSQNAVApphLGLsTQTVDSSQGSEYpYVIFsQTs-TAHu     
   consensus/80%                                                MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     
   consensus/70%                                                MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS     

                                                cov    pid 6121          .         .         :         .         .         .         .         2         .         .         .         . 6240
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      NNINRFNVAITRAQKGILCVMTSQALFESLEFTELSFTNYK---LQSQIVTGLFKDCSRETSGLSPAYAPTYVSVDDKYKTSDELCVNLNLPANVPYSRVISRMGFKLDATVPGYPKLFI     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      NNINRFNVAITRAQKGILCVMTSQALFESLEFTELSFTNYK---LQSQIVTGLFKDCSRETSGLSPAYAPTYVSVDDKYKTSDELCVNLNLPANVPYSRVISRMGFKLDATVPGYPKLFI     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                sNlNRFNVAITRAphGILClMospsLa-pLpFTpLphsphp...LQup.VTGLFKDCS+.hoGLpPs.APTalSVDsKaKTps.hss..slPtshsYpRlIShMGFKhshpVsGYPphFI     
   consensus/80%                                                CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     
   consensus/70%                                                CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI     

                                                cov    pid 6241          :         .         .         .         .         3         .         .         .         .         :         . 6360
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      -------------GFAV-------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      -------------GFAV-------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      TREEAVRQVRSWIGFDVEGAHASRNACGTNVPLQLGFSTGVNFVVQPVGVVDTEWGNMLTGIAARPPPGEQFKHLVPLMHKGAAWPIVRRRIVQMLSDTLDKLSDYCTFVCWAHGFELTS     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      TREEAVRQVRSWIGFDVEGAHASRNACGTNVPLQLGFSTGVNFVVQPVGVVDTEWGNMLTGIAARPPPGEQFKHLVPLMHKGAAWPIVRRRIVQMLSDTLDKLSDYCTFVCWAHGFELTS     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                TREEAlRpVRuWIGFDVEGsHAoRpAsGTNlPLQLGFSTGVNhVs.PsGhVDT..ss.hotluA+PPPG-QFKHLlPLMaKGhsWslVRh+IVQMLSDTLcpLSDhssFVhWAHGFELTS     
   consensus/80%                                                TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     
   consensus/70%                                                TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS     

                                                cov    pid 6361          .         .         .         4         .         .         .         .         :         .         .         . 6480
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      ASYFCKIGKEQKCCMCNRRAAAYSSPLQSYACWTHSCGYDYVYNPFFVDVQQWGYVGNLATNHDRYCSVHQGAHVASNDAIMTRCLAIHSCFIERVDWDIEYPYISHEKKLNSCCRIVER     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      ASYFCKIGKEQKCCMCNRRAAAYSSPLQSYACWTHSCGYDYVYNPFFVDVQQWGYVGNLATNHDRYCSVHQGAHVASNDAIMTRCLAIHSCFIERVDWDIEYPYISHEKKLNSCCRIVER     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                hpYFsKIG.EppCChCsRRAssaSos.poYACWpHShGaDYVYNPFhlDVQQWGasGNLtoNHDhYCpVHtsAHVASsDAIMTRCLAlHpCFlcRVDWsIEYPhIucEhKlNusCRhVp+     
   consensus/80%                                                MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     
   consensus/70%                                                MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH     

                                                cov    pid 6481          .         5         .         .         .         .         :         .         .         .         .         6 6600
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTAGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      NVVRAALLAGSFDKVYDIGNPKGIPIVDDPVVDWHYFDAQPLTR---KVQQLFYT-EDMASRFADGLCLFWNCNVPKYPNNAIVCRFDTRVHSEFNLPGCDGGSLYVNKHAFHTPAYDVS     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      NVVRAALLAGSFDKVYDIGNPKGIPIVDDPVVDWHYFDAQPLTR---KVQQLFYT-EDMASRFADGLCLFWNCNVPKYPNNAIVCRFDTRVHSEFNLPGCDGGSLYVNKHAFHTPAYDVS     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                .VV+AALLAspFshlaDIGNPKuI.hVspssV-W+aaDAQPhoc...KlppLFYo.tshus+FssGlCLFWNCNVs+YPsNuIVCRFDTRVhSphNLPGCDGGSLYVNKHAFHTPAaDhS     
   consensus/80%                                                MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     
   consensus/70%                                                MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS     

                                                cov    pid 6601          .         .         .         .         :         .         .         .         .         7         .         . 6720
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFIRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      AFRDLKPLPFFYYSTTPCEVHGNGSMIEDIDYVPLKSAVCITTCNLGGAVCRKHATEYREYMEAYNLVSASGFRLWCYKTFDIYNLWSTFTKVQGLENIAFNVVKQGHFIGVEGELPVAV     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      AFRDLKPLPFFYYSTTPCEVHGNGSMIEDIDYVPLKSAVCITACNLGGAVCRKHATEYREYMEAYNLVSASGFRLWCYKTFDIYNLWSTFTKVQGLENIAFNVVKQGHFIGVEGELPVAV     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                AFhsLK.LPFFYYSsoPCEsHGp.phlpDIDYVPLKSAsCITtCNLGGAVCR+HAsEYR.Yh-AYNhh.uuGFpLWsYKpFDhYNLWsTFh+lQuLENlAFNVVppGHF.G.pGElPVul     
   consensus/80%                                                AFVNLKQLPFFYYSDSPCESHGK.QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     
   consensus/70%                                                AFVNLKQLPFFYYSDSPCESHGK.QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI     

                                                cov    pid 6721          .         .         :         .         .         .         .         8         .         .         .         . 6840
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      VNDKIFTKSGVNDICMFENKTTLPTNIAFELYAKRAVRSHPDFKLLHNLQADICYKFVLWDYERSNIYGTATIGVCKYTDIDVNSALNIC------FDIRDNGSLEKFMSTPNAIFISDR     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      VNDKIFTKSGVNDICMFENKTTLPTNIAFELYAKRAVRSHPDFKLLHNLQADICYKFVLWDYERSNIYGTATIGVCKYTDIDVNSALNIC------FDIRDNGSLEKFMSTPNAIFISDR     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                lNsplaTKssssDlphFENKTTLPsNlAFELaAKRsl+shP-hKlLpNLtsDIshphVlWDYcRss.hthuTIGVCphTDIshpss.sIC......FDhRssGpl-hFhss.NulhIo-t     
   consensus/80%                                                INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     
   consensus/70%                                                INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG     

                                                cov    pid 6841          :         .         .         .         .         9         .         .         .         .         :         . 6960
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYK-EGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      KIKKYPCMVGPDYAYFNGAIIRDSDVVKQPVKFYLYKKVNNEFIDPTECIYTQSRSCSDFLPLSDMEKDFLSFDSDVFIKKYGLENYAFEHVVYGDFSHTTLGGLHLLIGLYKKQQEGHI     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      KIKKYPCMVGPDYAYFNGAIIRDSDVVKQPVKFYLYKKVNNEFIDPTECIYTQSRSCSDFLPLSDMEKDFLSFDSDVFIKKYGLENYAFEHVVYGDFSHTTLGGLHLLIGLYKKQQEGHI     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                plKth.s.VGPc.A.hNGshlhspsVhpQ...F.hYKKVss.h.p.sEshaTQSRshp-FhPhSpMEhDFLphs.D.FIc+Yt.EsYAFEHlVYGDFSHopLGGLHLLIGLhK+.pEu.h     
   consensus/80%                                                SVKGLQPSVGPKQASLNGVTLIGEAVKTQ...FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     
   consensus/70%                                                SVKGLQPSVGPKQASLNGVTLIGEAVKTQ...FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF     

                                                cov    pid 6961          .         .         .         0         .         .         .         .         :         .         .         . 7080
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      IMEEMLKGSSTIHNYFITETNTAAFKAVCSVIDLKLDDFVMILKSQDLGVVSKVVKVPIDLTMIEFMLWCKDGQVQTFYPRLQASADWKPGHAMPSLFKVQNVNLERCELANYKQSIPMP     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      IMEEMLKGSSTIHNYFITETNTAAFKAVCSVIDLKLDDFVMILKSQDLGVVSKVVKVPIDLTMIEFMLWCKDGQVQTFYPRLQASADWKPGHAMPSLFKVQNVNLERCELANYKQSIPMP     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                .hE-hl.hsSTl+NYFIT-spTuu.KsVCSVIDLhLDDFV.IlKSQDLuVVSKVVKVsIDhT.IpFMLWCKDGpVpTFYP+LQuStsWpPGhAMPsLaKhQph.LE+C-LtNYtpShshP     
   consensus/80%                                                ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     
   consensus/70%                                                ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP     

                                                cov    pid 7081          .         1         .         .         .         .         :         .         .         .         .         2 7200
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGMLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ---------------------------------------------------------------------------------------------------------NESGVLL--------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      RGVHMNIAKYMQLCQYLNTCTLAVPANMRVIHFGAGSDKGIAPGTSVLRQWLPTDAIIIDNDLNEFVSDADITLFGDCVTVRVGQQVDLVISDMYDPTTKNVTGSNESKALFFTYLCNLI     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ---------------------------------------------------------------------------------------------------------NESGVLL--------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      RGVHMNIAKYMQLCQYLNTCTLAVPANMRVIHFGAGSDKGIAPGTSVLRQWLPTDAIIIDNDLNEFVSDADITLFGDCVTVRVGQQVDLVISDMYDPTTKNVTGSNESKALFFTYLCNLI     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                +GlhMNlAKYhQLCQYLNThTLAVPhNMRVIHFGAGSDKGlAPGTuVLRQWLPTshlllDsDLN-FVSDAD.TLhGDCsTV+supphDLlISDMYDPpTKNVTtpN-SKthFFTYlCshI     
   consensus/80%                                                KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     
   consensus/70%                                                KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI     

                                                cov    pid 7201          .         .         .         .         :         .         .         .         .         3         .         . 7320
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      ------------------------------------------------------------------------------------------------------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      ------------------------------------------------------------------------------------------------------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQINGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      NNNLALGGSVAIKITEHSWSVELYELMGKFAWWTVFCTNANASSSEGFLLGINYLGTIKENIDGGAMHANYIFWRNSTPMNLSTYSLFDLSKFQLKLKGTPVLQLKESQINELVISLLSQ     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      ------------------------------------------------------------------------------------------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      NNNLALGGSVAIKITEHSWSVELYELMGKFAWWTVFCTNANASSSEGFLLGINYLGTIKENIDGGAMHANYIFWRNSTPMNLSTYSLFDLSKFQLKLKGTPVLQLKESQINELVISLLSQ     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                pppLALGGSVAIKITEHSWss-LYcLMG+FAWWTsFsTNsNASSSEuFLlGhNYLGp.+EpIsGhsMHANYIFWRNosPhpLSoYSLFDhSKF.LKL+GTsVhpLKEuQIN-hllSLLSp     
   consensus/80%                                                QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     
   consensus/70%                                                QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK     

                                                cov    pid 7321          .         .     ] 7346
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
 2 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
 3 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
 4 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
 5 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
 6 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
 7 ORF1a_Finland_29Jan2020                    61.9%  73.0%      --------------------------     
 8 ORF1a_China-Yunnan_17Jan2020               62.1%  73.2%      --------------------------     
 9 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
10 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
11 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
12 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
13 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
14 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
15 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
16 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
17 ORF1AB_China_11Jan2020                    100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
18 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
19 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
20 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
21 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
22 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
23 ORF1AB_USA-CA_27Jan2020                    99.9%  99.8%      GRLIIRENNRVVISSDVLVNN-----     
24 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      GRLIIRENNRVVISSDVLVNN-----     
25 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
26 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      GRLIIRENNRVVISSDVLVNN-----     
39 ORF1a_MERSctrl_SaudiArabia_01May2013       58.5%  21.1%      --------------------------     
40 ORF1AB_MERSctrl_SaudiArabia_01May2013      96.2%  45.0%      GKLLIRDNDTLSVSTDVLVNTYRKLR     
41 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.5%  21.1%      --------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    96.2%  45.0%      GKLLIRDNDTLSVSTDVLVNTYRKLR     
   consensus/100%                                               ..........................     
   consensus/90%                                                G+LlIR-NsplslSoDVLVNs.....     
   consensus/80%                                                GRLIIRENNRVVISSDVLVNN.....     
   consensus/70%                                                GRLIIRENNRVVISSDVLVNN.....     

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